Microsatellite analysis of genetic population structure in an endangered salmonid: the coastal cutthroat trout (Oncorhynchus clarki clarki)

The genetic population structure of coastal cutthroat trout ( Oncorhynchus clarki clarki ) in Washington state was investigated by analysis of variation in allele frequencies at six highly polymorphic microsatellite loci for 13 anadromous populations, along with one outgroup population from the Yellowstone subspecies ( O. clarki bouvieri) (mean heterozygosity = 67%; average number of alleles per locus = 24). Tests for genetic differentiation revealed highly significant differences in genotypic frequencies for pairwise comparisons between all populations within geographical regions and overall population subdivision was substantial ( F _ST = 0.121, R _ST = 0.093), with 44.6% and 55.4% of the among-population diversity being attributable to differences between streams ( F _SR = 0.054) and between regions ( F _RT = 0.067), respectively. Analysis of genetic distances and geographical distances did not support a simple model of isolation by distance for these populations. With one exception, neighbour-joining dendrograms from the Cavalli-Sforza and Edwards' chord distances and maximum likelihood algorithms clustered populations by physiogeographic region, although overall bootstrap support was relatively low (53%). Our results suggest that coastal cutthroat trout populations are ultimately structured genetically at the level of individual streams. It appears that the dynamic balance between gene flow and genetic drift in the subspecies favours a high degree of genetic differentiation and population subdivision with the simultaneous maintenance of high heterozygosity levels within local populations. Results are discussed in terms of coastal cutthroat trout ecology along with implications for the designation of evolutionarily significant units pursuant to the US Endangered Species Act of 1973 and analogous conservation units.     

Persistence of British natterjack toad Bufo calamita Laurenti (Anura: Bufonidae) populations despite low genetic diversity

Like other amphibians native to Britain, the natterjack toad Bufo calamita must have colonized the islands during the relatively short period between the end of the last glaciation and the separation of Britain from mainland Europe by rising sea levels. Unlike the other native amphibians, however, B. calamita is a habitat specialist at the north-westerly edge of its biogeographical range and for most of the 8000–10000 years since its colonization has probably been restricted to open dunes, heathlands and upper saltmarshes, as isolated populations in a few discrete areas of the country. We have investigated the genetic diversity and relatedness of six widely separated British natterjack populations by allozyme analysis, and shown that all have very low diversity (Overall P _95%= 2.7%, H = 0.004) by comparison with other anurans, including natterjack populations in mainland Europe and common frogs ( Rana temporaria , L) in Britain. Eighty percent of loci were fixed for the same allele in all six British natterjack populations and genetic differentiation between colonies was extremely low. The possible significance of these findings to the persistence of small isolated populations at range edges is discussed.     

Defining population boundaries: use of three Bayesian approaches with microsatellite data from British natterjack toads (Bufo calamita)

Defining boundaries between populations is often difficult in the absence of information about current levels of gene flow. Such definitions can be important, however, both for the understanding of population dynamics and for conservation planning. Recently developed Bayesian methods for analysing genetic data now provide a powerful approach to this problem. Natterjack toads Bufo calamita are endangered in Britain, where their distribution is restricted to four geographically discrete regions. In three of these regions the boundaries between populations are often uncertain. We therefore used Bayesian approaches with microsatellite data to try and define British natterjack population structure, and thus inform conservation management. A large sample of natterjack toads from all 38 locations in Britain where the species is native was genotyped at eight microsatellite loci. The genetic diversity of natterjack populations declined as a function of increasing latitude, echoing postglacial colonization dynamics. Comparisons of three assignment methods (structure, baps and geneland) generated some broad similarities but also some inconsistencies in the definitions of population structure, especially in the most complex region (south Cumbria). Implications of the analyses for the future conservation of Bufo calamita in Britain are discussed.     

Genetic variability in geographic populations of the natterjack toad (Bufo calamita)

Across altitudinal and latitudinal gradients, the proportion of suitable habitats varies, influencing the individual dispersal that ultimately can produce differentiation among populations. The natterjack toad (Bufo calamita) is distributed across a wide geographic range that qualifies the species as interesting for a geographic analysis of its genetic variability. Five populations of B. calamita in the Sierra de Gredos (Spain) were studied in an altitudinal gradient ranging from 750 to 2270 m using microsatellite markers. In addition, we analyzed the latitudinal genetic variation in B. calamita within a global European distribution using genetic diversity parameters (mean number of alleles per locus [M(a)] and expected heterozygosity [H(E)]) obtained from our results and those published in the literature. The low level of genetic differentiation found between populations of B. calamita (F(st) ranging from 0.0115 to 0.1018) and the decreases in genetic diversity with altitude (M(a) from 13.6 to 8.3, H(E) from 0.82 to 0.74) can be interpreted by the combined effects of discontinuous habitat, produced mainly by the high slopes barriers and geographic distance. In the latitudinal gradient, genetic diversity decreases from south to north as a consequence of the colonization of the species from the Pleistocene refugium. We conclude that the genetic variability in B. calamita along its wide altitudinal and latitudinal geographic distribution mainly reflects the colonization history of the species after the last glacial period.     

基于微卫星标记的中国东北地区灰飞虱遗传变异及种群遗传结构分析

【目的】本研究旨在明确我国东北地区灰飞虱Laodelphax striatellus种群遗传变异及种群遗传结构,阐明种群间遗传分化与基因流。【方法】利用9对微卫星引物对采自我国东北地区15个地理种群的375头灰飞虱样品进行测序与分析;利用GeneAlex6.51,GENEPOP4.0.9和STRUCTURE 2.3.4等软件分析灰飞虱地理种群间的遗传多样性、遗传分化、基因流及种群遗传结构。【结果】在所分析的375头灰飞虱个体中,各位点平均有效等位基因数Na=6.898;总体上,灰飞虱不同地理种群遗传多样性较高(平均观测杂合度Ho=0.548;平均期望杂合度He=0.582),各种群间基因流较低(Nm=0.660)。UPGMA聚类树、PCoA及STRCTURE分析结果表明,东北地区灰飞虱种群分为两分支:吉林(JL)和沈阳(SY2012,SY2013和SY2014)种群聚为一支;其余种群聚为一支。AMOVA分析结果表明,灰飞虱遗传变异主要来自种群内(87%),种群间变异水平较低(13%)。【结论】中国东北地区灰飞虱遗传多样性较高,不同地理种群存在一定程度的遗传分化,且基因交流较低,存在一定的种群遗传结构。     

Genetic differentiation of starling (Sturnus vulgaris: Aves) populations in New Zealand and Great Britain

Several hundred starlings (Sturnus vulgaris) were introduced to New Zealand from Great Britain during1860–1880. Allozymic variation at 24 loci was analysed in winter populations sampled at six localities in each country. New Zealand samples had fewer alleles per locus but the same mean heterozygosity (3% per locus) and proportion of polymorphic loci as did British samples. Winter populations in Britain contain European migrants and were genetically homogeneous. Paradoxically, genetic distances among derived New Zealand populations, and between New Zealand and Great Britain were much greater, similar in magnitude to those observed among allopatric populations in other avian species. The geographical pattern of genetic variation in New Zealand suggests that reproductive isolation of populations and random drift have contributed to the development of population differentiation.     

澜沧江中上游光唇裂腹鱼四个地理群体遗传多样性分析

利用简化基因组测序对澜沧江中上游的苗尾-功果桥库区、黄登-大华桥库区、里底江段和乌弄龙江段4个地理群体60个光唇裂腹鱼(Schizothorax lissolabiatus Tsao)样本进行了简化基因组测序, 平均测序深度255.26X, Q30为94.96%, 平均GC含量为39.80%; 测序获得多态性SLAF标签252623个, SNP标记1151083个, 其中, SNP平均完整度为36.66%, SNP平均杂合率为9.5%; 通过测序结果进行遗传多样性分析, 结果表明, 观测等位基因数均为2, 平均期望等位基因数为1.4211—1.5029, 平均观测杂合度为0.2381—0.3131, 平均期望杂合度为0.2690—0.3115, 平均多样性指数为0.2868—03248, 平均香浓指数为0.4269—0.481, 平均次要基因频率(MAF)为0.1854—0.2216, 平均多态信息含量(PIC)为0.2237—0.2553; AMOVA分析结果显示, 在总的变异中, 89.73%的遗传变异来自群体内部, 10.27%的遗传变异来自于群体间, 群体间遗传分化指数在–0.0150—0.1299(P<0.05), 表明群体间存在不同程度的分化。4个群体间遗传距离为0.05—0.15, UPGMA聚类表明, 苗尾-功果桥库区、黄登-大华桥库区和里底3个地理群体相互交叉聚类, 乌弄龙地理群体单独聚为一类。综上, 4个群体的遗传多样性处于中等水平, 遗传距离及聚类结果与试验群体地理距离基本相符, 研究结果将为光唇裂腹鱼种质资源评价与保护提供参考依据。     

中华鳖5个群体遗传多样性的微卫星分析

利用微卫星分子标记技术对洞庭(DT)、黄河(HH)、黄沙(HS)、日本(RB)以及洞庭(DT)与黄河(HH)的杂交子代(DT♀×HH♂)绿卡(LK)5个中华鳖群体的150个个体进行遗传多样性分析。11对微卫星引物扩增出的等位基因数为3～6个,平均等位基因数为4.1818。5个种群相比,绿卡(LK)的平均有效等位基因数、平均期望杂合度、平均观测杂合度和平均多态信息含量最高,分别是2.3969、0.5274、0.5545和0.4660。对种群间的遗传分化分析表明,黄河(HH)和洞庭(DT)之间的遗传分化最小,为0.0233,而洞庭(DT)和日本(RB)之间的遗传分化最大,为0.0969。基于Nei’s遗传距离构建的UPGMA系统进化树显示黄河(HH)和洞庭(DT)及其子代绿卡(LK)亲缘关系较近,而与黄沙(HS)和日本(RB)的亲缘关系较远,最远的为日本(RB)群体。     

微卫星DNA标记探讨镜鲤的种群结构与遗传变异

采用30个微卫星分子标记, 对5个镜鲤群体的观测杂合度(^H_o)、期望杂合度(^H_e)、多态信息含量(PIC)和有效等位基因数(^A_e)等进行了遗传检测, 根据基因频率计算遗传相似系数和Nei氏标准遗传距离, 以c2检验估计Hardy-Weinberg平衡, 以近交系数(FST)和基因流(Nm)分析群体的遗传分化。同时, 使用PHYLIP3.63软件绘制基于Nei氏标准遗传距离的UPGMA聚类图, 并进行bootstrap自举检验验证进化树的可靠性。在德国镜鲤选育系(Scattered Cyprinus carpio L.)和来自4个不同养殖场(松浦、东岗、奉城和辽中)的德国镜鲤群体中共检测到7 083个扩增片段, 长度在102 ~ 446 bp之间, 在群体内扩增出等位基因1~16个不等, 共计356个等位基因。结果表明: (1)5个群体检测的有效等位基因数在1.07~12.30个不等, 平均多态信息含量为0.74、0.74、0.69、0.75和0.75, 无偏期望杂合度的平均值为0.74、0.78、0.70、0.76和0.78, 说明这几个群体属于高度多态, 遗传多样性水平较高。(2)群体间相似系数在0.52以上, 相似性较高。聚类分析显示, 东岗、奉城和辽中3个养殖场的德国镜鲤群体聚类成一个分支, 而德国镜鲤选育系与松浦群体聚类成另一分支。聚类的先后与它们在地理分布上距离远近有一定的相关性。(3)在与功能基因相关的多个微卫星基因座位上, 扩增产物呈现不同程度的缺失现象, 这些无效等位基因的产生可能与结构基因在育种中受到人工选择的影响较大有关。     

A microsatellite analysis of natterjack toad, Bufo calamita, metapopulations

Although it is widely recognised that spatial subdivision of populations is common in nature, there is no consensus as to how metapopulation dynamics affect genetic diversity. We investigated the genetic differentiation of natterjack toads, Bufo calamita , in three regions of Britain where habitat continuity indicated the likely occurrence of extensive metapopulations. Our intention was to determine whether genetic analysis supported the existence of metapopulation structures, if so of what type, and to identify barriers to migration between subpopulations. Allele frequencies were determined across eight polymorphic microsatellite loci for a total of 24 toad subpopulations at three separate sites. Genetic differentiation was assessed using five measures of genetic distance, notably F _ST , R _ST , Nei's standard distance D _s , Δμ² and the Cavalli-Sforza chord distance D _c . B. calamita exhibited small but significant levels of genetic differentiation between subpopulations in all three study areas, and genetic and geographic distance correlations indicated isolation-by-distance effects in all three cases. The effects on correlation strengths of compensation for positive (sea, rivers, urban development) and negative (pond clusters) barriers to toad migration between the subpopulations in each area were also determined. D _c , a measure which assumes that differentiation is caused by drift with negligible mutation effect, yielded the most plausible interpretation of metapopulation structures. Overall the patterns of genetic variation suggested the existence of a mixed metapopulation model for this species, with high levels of gene flow compatible with one version of the classical model but often supported by particularly stable subpopulations as in the mainland-island model.     

Genetic variability in Tunisian populations of faba bean (<Emphasis Type="Italic">Vicia faba</Emphasis> L. var. <Emphasis Type="Italic">major</Emphasis>) assessed by morphological and SSR markers

The genetic diversity of 21 faba bean populations was examined using morphological and molecular markers. DNA was extracted from 189 individuals and 8 microsatellite markers were genotyped individually in these 21 populations. A total of 53 alleles were obtained in all populations, with an average of 6.62 alleles per locus. The expected and observed heterozygosity was 0.38 and 0.62 respectively. The average polymorphism index content of SSR markers was 0.61, ranging from 0.31 to 0.81. The unweighted pair group method with arithmetic mean dendrogram clustered all the populations into two groups, each for them subdivided into 3 sub-groups according to geographical origin. Morphological variation showed that the populations were not grouped according to their geographical origin. Therefore, patterns of differentiation of morphological traits did not coincide with molecular differentiation, indicating that morphological variation does not reflect genetic subdivision in studied faba bean populations. Analysis of molecular variance revealed high levels of genetic variation (83%) within population and provides a good base for designing genetic improvement programs. The result of Principal Component Analysis (PCA) revealed that three dimensional principal components (PC1, PC2 and PC3) contributed 40.56% of the total variability and accounted with values of 20.64, 11.22 and 8.70%, respectively. Cluster analysis based on PCA indicated three separate groups of populations. The genetic relationships found between the 21 populations samples were the same in both the PCA and STRUCTURE analysis which support the results observed. These data may serve as a foundation for the development of faba bean breeding programs.     

微卫星DNA标记分析野生鲤鱼群体的遗传多样性

利用30个微卫星分子标记对海南鲤(HN)、长江鲤(CY)、月亮湖鲤(YL)、黑龙江鲤(FY)、呼伦湖鲤(ZL)、贝尔湖鲤(BR)6个野生鲤鱼群体的观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)和有效等位基因数(Ae)等进行了遗传检测,根据基因频率计算遗传相似系数和Nei氏标准遗传距离,χ2检验估计Hardy-Weinberg平衡,用近交系数(FST)和基因流(Nm)分析群体的遗传分化及其来源。同时,使用PHYLIP3.63软件绘制基于Nei氏标准遗传距离的UPGMA进化树。6个群体共检测到8,136个扩增片段,长度在125bp～414bp,30个基因座扩增出等位基因数从3～13个不等,共计210个等位基因,平均每个基因座扩增得到7个等位基因。结果显示:(1)6个野鲤群体的多态性指标均适中,多态信息含量依次0.44、0.52、0.53、0.57、0.63和0.64,有效等位基因数1.04～4.72个不等,平均有效等位基因数依次为2.19、2.60、2.42、2.43、2.45和2.33,无偏期望杂合度平均值为0.50、0.59、0.56、0.56、0.57和0.54;(2)遗传相似系数BR与ZL最高(0.8511),BR与HN最低(0.6688),聚类结果与地理分布呈一定相关性。     

长江下游地区4个克氏原螯虾群体的遗传多样性分析

为了对长江下游地区克氏原螯虾(Procambarus clarkii)群体的遗传多样性状况进行本底调查, 本文利用17对微卫星引物对南京(NJ)、盱眙(XY)、合肥(HF)、南昌(NC)4个克氏原螯虾地理群体进行了遗传多样性研究。结果表明, 4个地理群体的平均观测杂合度为0.4322–0.4826、平均期望杂合度为0.4024–0.6121、平均多态信息含量为0.3408–0.5624, 4个克氏原螯虾群体的遗传多样性处于中等水平, 其中南京群体遗传多样性最高, 合肥群体最低; 4个克氏原螯虾群体的基因流为1.3729–5.9161, 遗传分化指数为0.0405–0.1540, 群体间基因流水平较高, 群体间遗传分化程度较小。聚类结果显示4个群体可分为2支: 南京、南昌、盱眙三个群体聚为一支, 合肥群体独自成一支。以上结果将为克氏原螯虾遗传育种、资源保护和利用提供一定的理论依据。     

内蒙古亚洲小车蝗种群遗传多样性的微卫星分析

亚洲小车蝗Oedaleus asiaticus Bei-Bienko是我国北方草原和农牧交错区主要的害虫之一。为了从分子水平评价内蒙古地区亚洲小车蝗种群的遗传多样性和种群间遗传分化, 本文采用8对微卫星引物对内蒙古15个地点的亚洲小车蝗种群进行遗传多样性分析。结果表明： 各位点有效等位基因数为3.4517~13.2881, 多态信息含量值为0.5601~0.8563, Shannon氏多样性指数在0.7018~4.1789之间。15个种群的平均期望杂合度为0.6836, Nei氏期望杂合度为0.5303~0.6513, 群体遗传距离为0.1092~0.4235, 群体分化率Fst平均值为0.1612, 基因流Nm平均值为1.6164。8个微卫星位点均具有较高的多态性, 各种群间的遗传分化水平较大, 基因交流程度中等, 个体间的遗传变异大于种群间的遗传变异。15个不同地点的亚洲小车蝗种群根据遗传距离共聚为6支。种群间遗传分化与地理距离呈正相关关系。高山和沙漠对不同地区亚洲小车蝗种群的迁移具有阻碍作用, 可能是形成遗传分化的主要原因。研究结果从分子水平探索不同地区亚洲小车蝗种群间的内在联系, 为制定亚洲小车蝗的综合治理策略提供了分子生物学的基础资料。     

华东地区中华蜜蜂六地理种群的遗传多样性及遗传分化

目的】利用23对微卫星标记对来自于南昌、黄山、桐庐、费县、宜兴、武夷山6个华东地区的中华蜜蜂Apis cerana cerana种群进行遗传多样性及遗传分化分析。【方法】通过计算多态信息含量、平均杂合度、等位基因数、遗传距离、基因流、F 统计量等参数, 评估各中蜂种群遗传多样性和各种群间遗传分化。【结果】各座位的等位基因数为5（A014）至30（AP043）。所有种群均显示较高水平的期望杂合度, 其中, 武夷山中蜂最低, 为0.4280; 南昌中蜂最高, 为0.6329。各中蜂种群间存在极显著的遗传分化, 平均分化系数(Fst)为0.344。基于Nei氏遗传距离运用NJ聚类法将6个中蜂种群划分为3类。【结论】华东6个中蜂种群的遗传多样性较高, 遗传分化显著; 分析遗传分化与地理距离的关系发现, 华东6个中蜂种群间的遗传分化与地理距离不存在显著相关。     

Allozyme Diversity in Populations of Cymbidium goeringii (Orchidaceae)

Abstract: Using 14 allozyme loci, we investigated levels of genetic diversity within populations, and degree of genetic divergence among 24 populations of Cymbidium goeringii (Orchidaceae) in Korea and Japan. Cymbidium goeringii maintains high levels of genetic diversity both at population (mean expected heterozygosity, H _e = 0.238) and species levels (0.260). Means of H _e found in 24 populations were not significantly different from each other. About 90 % of the total variation in the species is common to all populations (mean G _ST = 0.108). No unique allele was found in any population. The indirect estimate of gene flow based on the mean G _ST was high ( Nm = 2.06). Nei's genetic identities for pairs of populations had high values (mean = 0.974 [SD = 0.013]). The Mantel-Z test showed a significant correlation between genetic distance and geographic distance. However, the mean G _ST value between 17 populations in Korea and seven Japanese populations was relatively low (0.029), even though the land connection between the southern Korean peninsula and southern Japanese archipelagos has not existed since the middle Pleistocene. Large numbers of small seeds of C. goeringii might travel long distances by wind from populations to populations both in Korea and Japan, increasing genetic diversity within populations and maintaining low genetic differentiation among populations.     

Genetic diversity of Asian water buffalo (Bubalus bubalis): microsatellite variation and a comparison with protein-coding loci

Twenty-one microsatellite loci in 11 populations of Asian water buffalo (eight swamp, three river type) were analysed and, within and among populations, genetic variability was compared with results from 25 polymorphic protein-coding loci. Within-population mean heterozygosity ranged from 0·380–0·615, approximately twice that estimated from the protein-coding loci (0·184– 0·346). Only eight significant departures from Hardy–Weinberg equilibrium (involving four loci) were detected; global tests showed significant heterozygote deficiencies for these four loci. Non-amplifying alleles are likely to be segregating in some or all populations for one of these loci, and probably for the other three. There was significant differentiation between the swamp and river types of water buffalo, and among populations within each buffalo type. Estimates of θ (measure of population differentiation) for each locus for the eight swamp populations were all highly significant (mean θ = 0·168 ± 0·018). Mean θ for protein-coding loci was not significantly different (0·182 ± 0·041). The variance among protein-coding loci was significantly higher than among microsatellite loci, suggesting balancing selection affecting allele frequencies at some protein-coding loci. Genetic distances show clear separation of the swamp and river types, which were estimated to have diverged at least 10 000–15 000 years ago. The topology of the swamp populations’ microsatellite tree is consistent with their geographical distribution and their presumed spread through south-east Asia. By contrast, the tree based on the protein-coding loci distances is quite different, being clearly distorted by a bottleneck effect in one population, and possibly in at least two others. As many domestic livestock breeds are possibly descended from small numbers of founders, microsatellite-based trees are to be preferred in assessing breed genetic relationships.     

Genetic diversity and differentiation of Acanthoscelides obtectus Say (Coleoptera: Bruchidae) populations in China

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Geographical partitioning of goat diversity in Europe and the Middle East

Thirty microsatellite markers were analysed in 1426 goats from 45 traditional or rare breeds in 15 European and Middle Eastern countries. In all populations inbreeding was indicated by heterozygosity deficiency (mean FIS = 0.10). Genetic differentiation between breeds was moderate with a mean FST value of 0.07, but for most (c. 71%) northern and central European breeds, individuals could be assigned to their breeds with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed at least four discrete clusters: eastern Mediterranean (Middle East), central Mediterranean, western Mediterranean and central/northern Europe. About 41% of the genetic variability among the breeds could be explained by their geographical origin. A decrease in genetic diversity from the south-east to the north-west was accompanied by an increase in the level of differentiation at the breed level. These observations support the hypothesis that domestic livestock migrated from the Middle East towards western and northern Europe and indicate that breed formation was more systematic in north-central Europe than in the Middle East. We propose that breed differentiation and molecular diversity are independent criteria for conservation.     

蒙古沙葱萤叶甲种群遗传多样性的微卫星分析

【目的】沙葱萤叶甲 Galeruca daurica (Joannis)是一种近年来在内蒙古草原上猖獗成灾的新害虫,本研究旨在明确内蒙古沙葱萤叶甲不同地理种群间的遗传分化和基因交流程度。【方法】应用5对微卫星引物分析了沙葱萤叶甲8个地理种群的遗传多样性、基因流和遗传分化。【结果】5个位点等位基因数为10~18,有效等位基因数为9.2796~16.0388,多态信息含量值为0.6760~0.8985,期望杂合度为0.3430~0.5284,说明所选5个微卫星位点均为高度多态性位点。8个种群的期望杂合度为0.2216~0.3701,平均值为0.2680;种群间遗传分化系数为0.1244~0.4116,平均值为0.2521;种群间基因流为0.3574~1.7596,平均值为0.9622。8个地理种群根据遗传距离聚为3个分支,遗传距离与地理距离呈显著的正相关关系 (r=0.4854,P=0.0180)。【结论】沙葱萤叶甲种群遗传多样性低,不同地理种群之间基因流较小,遗传分化程度高;沙葱萤叶甲迁移能力弱和地理阻碍可能是限制其基因交流和导致遗传高度分化的主要原因。